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Uehata T, Yamada S, Ori D, Vandenbon A, Giladi A, Jelinski A, Murakawa Y, Watanabe H, Takeuchi K, Toratani K, Mino T, Kiryu H, Standley DM, Tsujimura T, Ikawa T, Kondoh G, Landthaler M, Kawamoto H, Rodewald HR, Amit I, Yamamoto R, Miyazaki M, Takeuchi O. Regulation of lymphoid-myeloid lineage bias through regnase-1/3-mediated control of Nfkbiz. Blood 2024; 143:243-257. [PMID: 37922454 PMCID: PMC10808253 DOI: 10.1182/blood.2023020903] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 11/05/2023] Open
Abstract
ABSTRACT Regulation of lineage biases in hematopoietic stem and progenitor cells (HSPCs) is pivotal for balanced hematopoietic output. However, little is known about the mechanism behind lineage choice in HSPCs. Here, we show that messenger RNA (mRNA) decay factors regnase-1 (Reg1; Zc3h12a) and regnase-3 (Reg3; Zc3h12c) are essential for determining lymphoid fate and restricting myeloid differentiation in HSPCs. Loss of Reg1 and Reg3 resulted in severe impairment of lymphopoiesis and a mild increase in myelopoiesis in the bone marrow. Single-cell RNA sequencing analysis revealed that Reg1 and Reg3 regulate lineage directions in HSPCs via the control of a set of myeloid-related genes. Reg1- and Reg3-mediated control of mRNA encoding Nfkbiz, a transcriptional and epigenetic regulator, was essential for balancing lymphoid/myeloid lineage output in HSPCs in vivo. Furthermore, single-cell assay for transposase-accessible chromatin sequencing analysis revealed that Reg1 and Reg3 control the epigenetic landscape on myeloid-related gene loci in early stage HSPCs via Nfkbiz. Consistently, an antisense oligonucleotide designed to inhibit Reg1- and Reg3-mediated Nfkbiz mRNA degradation primed hematopoietic stem cells toward myeloid lineages by enhancing Nfkbiz expression. Collectively, the collaboration between posttranscriptional control and chromatin remodeling by the Reg1/Reg3-Nfkbiz axis governs HSPC lineage biases, ultimately dictating the fate of lymphoid vs myeloid differentiation.
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Affiliation(s)
- Takuya Uehata
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shinnosuke Yamada
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Daisuke Ori
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Alexis Vandenbon
- Laboratory of Tissue Homeostasis, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Amir Giladi
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Adam Jelinski
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Yasuhiro Murakawa
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
| | - Hitomi Watanabe
- Laboratory of Integrative Biological Sciences, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Kazuhiro Takeuchi
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
| | - Kazunori Toratani
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takashi Mino
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hisanori Kiryu
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Daron M. Standley
- Department of Genome Informatics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Tohru Tsujimura
- Department of Pathology, Hyogo College of Medicine, Hyogo, Japan
| | - Tomokatsu Ikawa
- Division of Immunology and Allergy, Research Institute for Biomedical Sciences, Tokyo University of Science, Chiba, Japan
| | - Gen Kondoh
- Laboratory of Integrative Biological Sciences, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Markus Landthaler
- RNA Biology and Posttranscriptional Regulation, Max Delbrück Center for Molecular Medicine Berlin, Berlin Institute for Molecular Systems Biology, Berlin, Germany
| | - Hiroshi Kawamoto
- Laboratory of Immunology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Hans-Reimer Rodewald
- Division for Cellular Immunology, German Cancer Research Center, Heidelberg, Germany
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Ryo Yamamoto
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
| | - Masaki Miyazaki
- Laboratory of Immunology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Osamu Takeuchi
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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Lopez R, Li B, Keren-Shaul H, Boyeau P, Kedmi M, Pilzer D, Jelinski A, Yofe I, David E, Wagner A, Ergen C, Addadi Y, Golani O, Ronchese F, Jordan MI, Amit I, Yosef N. DestVI identifies continuums of cell types in spatial transcriptomics data. Nat Biotechnol 2022; 40:1360-1369. [PMID: 35449415 DOI: 10.1038/s41587-022-01272-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 03/07/2022] [Indexed: 11/09/2022]
Abstract
Most spatial transcriptomics technologies are limited by their resolution, with spot sizes larger than that of a single cell. Although joint analysis with single-cell RNA sequencing can alleviate this problem, current methods are limited to assessing discrete cell types, revealing the proportion of cell types inside each spot. To identify continuous variation of the transcriptome within cells of the same type, we developed Deconvolution of Spatial Transcriptomics profiles using Variational Inference (DestVI). Using simulations, we demonstrate that DestVI outperforms existing methods for estimating gene expression for every cell type inside every spot. Applied to a study of infected lymph nodes and of a mouse tumor model, DestVI provides high-resolution, accurate spatial characterization of the cellular organization of these tissues and identifies cell-type-specific changes in gene expression between different tissue regions or between conditions. DestVI is available as part of the open-source software package scvi-tools ( https://scvi-tools.org ).
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Affiliation(s)
- Romain Lopez
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley CA, USA
| | - Baoguo Li
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Hadas Keren-Shaul
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Pierre Boyeau
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley CA, USA
| | - Merav Kedmi
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - David Pilzer
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Adam Jelinski
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Ido Yofe
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Eyal David
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Allon Wagner
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley CA, USA
| | - Can Ergen
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley CA, USA
| | - Yoseph Addadi
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Ofra Golani
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Franca Ronchese
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Michael I Jordan
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel.,Department of Statistics, University of California, Berkeley, Berkeley CA, USA
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel.
| | - Nir Yosef
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley CA, USA. .,Center for Computational Biology, University of California, Berkeley, Berkeley CA, USA. .,Chan Zuckerberg Biohub, San Francisco CA, USA. .,Ragon Institute of MGH, MIT and Harvard, Cambridge MA, USA.
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Cohen B, Tempelhof H, Raz T, Oren R, Nicenboim J, Bochner F, Even R, Jelinski A, Eilam R, Ben-Dor S, Adaddi Y, Golani O, Lazar S, Yaniv K, Neeman M. BACH family members regulate angiogenesis and lymphangiogenesis by modulating VEGFC expression. Life Sci Alliance 2020; 3:e202000666. [PMID: 32132179 PMCID: PMC7063472 DOI: 10.26508/lsa.202000666] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 02/23/2020] [Accepted: 02/24/2020] [Indexed: 12/23/2022] Open
Abstract
Angiogenesis and lymphangiogenesis are key processes during embryogenesis as well as under physiological and pathological conditions. Vascular endothelial growth factor C (VEGFC), the ligand for both VEGFR2 and VEGFR3, is a central lymphangiogenic regulator that also drives angiogenesis. Here, we report that members of the highly conserved BACH (BTB and CNC homology) family of transcription factors regulate VEGFC expression, through direct binding to its promoter. Accordingly, down-regulation of bach2a hinders blood vessel formation and impairs lymphatic sprouting in a Vegfc-dependent manner during zebrafish embryonic development. In contrast, BACH1 overexpression enhances intratumoral blood vessel density and peritumoral lymphatic vessel diameter in ovarian and lung mouse tumor models. The effects on the vascular compartment correlate spatially and temporally with BACH1 transcriptional regulation of VEGFC expression. Altogether, our results uncover a novel role for the BACH/VEGFC signaling axis in lymphatic formation during embryogenesis and cancer, providing a novel potential target for therapeutic interventions.
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Affiliation(s)
- Batya Cohen
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Hanoch Tempelhof
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Tal Raz
- Koret School of Veterinary Medicine, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Roni Oren
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Julian Nicenboim
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Filip Bochner
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Ron Even
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Adam Jelinski
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Raya Eilam
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Shifra Ben-Dor
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Yoseph Adaddi
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Ofra Golani
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Shlomi Lazar
- Department of Pharmacology, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Karina Yaniv
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Michal Neeman
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
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Yofe I, Jelinski A, Solomon I, Landsberger T, de Massy MR, Peggs K, Quezada S, Amit I. Abstract A101: Single-cell analysis reveals the pivotal role of the innate immune compartment in aCTLA-4 antitumor response. Cancer Immunol Res 2020. [DOI: 10.1158/2326-6074.tumimm19-a101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Immunotherapies have revolutionized and continue to revolutionize cancer patient care; however, much of our understanding of the mechanism of action of these therapies is currently limited. The accumulation of regulatory T cells (Tregs) in the tumor hampers antitumor activity and correlates with bad prognosis in several human cancers. Anti-CTLA-4 monoclonal antibodies (mAbs) have been extensively studied, and their activity depends both on the blockade of the CTLA-4 coinhibitory molecule, as well as the intratumoral depletion of Tregs, increasing effector cell abundance, and favoring tumor rejection. Fc-gamma receptor (FcgR) coengagement has been proven to be important for the action of aCTLA-4, in addition to its Treg-depleting activity via antibody-dependent cellular cytotoxicity (ADCC); however, it is unclear what are the cellular changes involved. We therefore wished to dissect the differences between aCTLA-4 mIgG1, an antibody that only blocks the CTLA-4 receptor, and aCTLA-4 mIgG2a, which has a dual activity of both blocking the receptor and depleting Tregs. To address this, we performed single-cell RNA-seq of infiltrating leukocytes from tumors in mice treated with aCTLA-4 mIgG1, mIgG2a, or left untreated (UT). This high-resolution comparison revealed unique cellular profiles generated by each treatment. While the blocking-only mIgG1 was similar to UT, mIgG2a with ADCC effector function demonstrated major changes. Tumors in mIgG2a treated mice showed an immediate decline of immune suppressive macrophages, and the emergence of proinflammatory monocytes, as well as NK cells and naive CD8 T cells. In addition, mIgG2a-treated mice displayed a gradual increase of CD4 T-cell subsets throughout treatment. Finally, a vast tissue repair signature was observed in later time points of aCTLA-4 mIgG2a treatment, comprising MRC1+ macrophages, neutrophils, and myeloid-derived suppressor cells (MDSCs), while CD8 T-cell abundance declined. In summary, our findings provide an in-depth view of the differences in mechanisms of action between an aCTLA-4 blocking mAb and an optimized blocking-depleting mAb, underscoring how FcgRs coengagement leads to enhanced antitumor response via the innate immune compartment.
Citation Format: Ido Yofe, Adam Jelinski, Isabelle Solomon, Tomer Landsberger, Marc Robert de Massy, Karl Peggs, Sergio Quezada, Ido Amit. Single-cell analysis reveals the pivotal role of the innate immune compartment in aCTLA-4 antitumor response [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2019 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2020;8(3 Suppl):Abstract nr A101.
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Affiliation(s)
- Ido Yofe
- 1Weizmann Institute of Science, Rehovot, Israel,
| | | | - Isabelle Solomon
- 2University College London Cancer Institute, London, United Kingdom
| | | | | | - Karl Peggs
- 2University College London Cancer Institute, London, United Kingdom
| | - Sergio Quezada
- 2University College London Cancer Institute, London, United Kingdom
| | - Ido Amit
- 1Weizmann Institute of Science, Rehovot, Israel,
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